Having lost 2-3 early this year in Chad, the home side badly needed a win and they delivered in style to progress 4-3 on aggregate.
Winger John Banda claimed his second goal in as many matches on 31 minutes while Joseph Kamwendo wrapped up the win with a terrific goal on 72 minutes.
With First Gentleman retired Chief Justice Richard Banda watching from the VIP seat, Malawi did not play with fluency like they did against Nigeria in last week's World Cup qualifier that ended 1-1, but simply got the business done.
A very physical Chad visibly came to contain Malawi with long balls and earlier dominance that never worked, save for leaving the hosts with two injury casualties, goal scorer John Banda and Spain based striker Robin Ngalande.
John Banda, who rescued Malawi in the dying minutes against Nigeria last week, put Malawi, who had missed a penalty through Kamwendo in the 29th minute, ahead with a powerful shot.
Banda had cut from the right wing to power his shot into the net with his left and grant coach Phiri relief at the stadium.
Half time ended with the hosts leading 1-0. There were still some nerves after break, goalkeeper Simplex Nthala stretching full length to keep out Karl Max Karmoure's long range shot then again denying defender Kelvin Niclaise Tatila’s point-blank shot.
But with Banda limping off for debutant Peter Pindani followed by Ngalande who came off for John Banda's elder brother Frank Banda, Malawi stepped up a gear.
Receiving a square pass from Black Leopards midfielder Dave Banda, the former Orlando Pirates man Kamwendo released a rocket that hit the roof of the net to spark celebrations.